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my $first_counter = 0;
my $second_counter = 0;
...

print "First counter: $first_counter\n";
print "Second counter: $second_counter\n";

my @real_count = (0,0,0,0);
my $sequence = "GGGGGGGAGAAAAAAAAAAAAAAAGAAGGA";
...
foreach (@real_count) {
    print "$_\n";
}